Mass Effect 3 - Alternate Ending
by SuperGenX
Summary: Although the extended cut of Mass Effect 3 was alright, something was missing. Features a final boss fight, and Shepard finally sticking it to that Starchild!


**Hello Children, and welcome to my Mass Effect 3 Alternate Ending!**

**I actually started writing this before the extended cut came out. At the time I was pretty pissed about the ending. However, the extended cut did bring me satisfaction and I can now say that Mass Effect 3 had an "ok" ending.**

**The main reason I decided to finish this is because I'm bored. The second reason is because I'm still trying to write the outline of my "Halo 4: A Rip in Time" story. Because at the end… I'm going to do this thing… when I BLOW YUR FUCKIN MIND.**

**But first I have to figure out how to get there, so in the mean time I thought I would feed my hungry viewers with this story. It's only one chapter (as of right now, that might change depending on the feedback) so it didn't take me very long.**

**Anyway, I hope you enjoy my Mass Effect 3 Alternate Ending!**

* * *

Shepard staggers to the top of the ramp, each step bringing another flush of pain. He comes upon a room he's never seen before and notices Anderson leaning on some kind of console. "Anderson?" Shepard asks.

Anderson slowly turns around and faces Shepard, whom instantly realizes that something is wrong. "Shepard… I can't…" Anderson tries to speak, but some unseen force tightens its grip around his neck.

"I underestimated you, Shepard." Says a familiar voice from behind.

Shepard recognizes the voice; it's a voice he despises. He tries to turn around to face the Illusive Man, but his body is suddenly held in place by invisible shackles. "What the…?" Shepard chokes.

"I warned you Shepard." The Illusive man starts. "Control is the means to survival. Control of the Reapers… and you, if necessary."

Anderson struggles to break free of the invisible influence over his body. "No…. they're controlling you!" He barks.

The Illusive man laughs. "I don't think so Admiral."

"What makes you think… you can control them?" Shepard asks. The Illusive Man looks over with a look of pity.

"Because Shepard, just look what I can do with you. You are helpless to my influence!" The Illusive Man smirks at the thought.

"Controlling me… is a lot different from controlling a Reaper." Shepard says.

"Oh please. Have a LITTLE faith Shepard." The Illusive Man requests. He walks over to the console and faces Shepard again. "When humanity discovered the Mass Relays… when we learned there was more to the galaxy then we imagined… there were some who thought the Relays should be destroyed." The Illusive man explains. "They were scared of what we'd find. Terrified of what we might let in."

"But look at what we have achieved! Since that discovery, we've advanced more than the last 10,000 years combined!" He claims excitedly. "And the Reapers will do the same for us again. A thousand fold!"

Shepard feels the influence inside him grow, and he points his weapon at Anderson against his will. "But only if we can harness their ability to control!" The Illusive Man continues. "We can-"

"Bullshit!" Anderson interrupts. "We destroy them, or they destroy us!"

"And waste this opportunity? Never!" The Illusive Man fires back.

"You're playing with things you don't understand!" Shepard attempts to reason. "With power you shouldn't be able to use!"

"I... don't believe that." The Illusive Man states. "If we can control it, why shouldn't it be ours?"

"Because…" Shepard thinks quickly. "We're not ready." He says.

"No. This is the way humanity must evolve!" The Illusive Man claims.

"There's always another way!" Anderson says.

The Illusive Man ignores them. "I have dedicated my life to understanding the Reapers, and I know with certainty that the Crucible allows me to control them!"

"And then what?" Shepard asks. "If you succeed, what will you do then?"

The Illusive Man sighs, knowing that a demonstration will change their minds. "Look at the power they wield! Look at what they can do!"

The Illusive Man glows with power and his skin starts to peel away. Where there should be organs and muscle is metal and wiring. His form grows in size until he is three times the size he was before. The only thing that remains of his old self is his glowing blue eyes.

"I took what I wanted from them." The Illusive man argues. "Made it my own! This isn't about you or me, this is about things much bigger than any of us!" Shepard feels the influence trying to invade his mind.

"Don't listen to him!" Anderson pleads.

The Illusive Man swings his massive arm in a sweeping motion and it connects with Anderson's torso. Anderson is sent flying back and tosses a canister of medigel at Shepard before falling off the ledge. Shepard grabs the canister and applies the medigel. He instantly feels invigorated and back to full strength.

He looks at the Illusive Man, blood boiling. "The Reapers have to be destroyed, and if I have to kill you to do it, then I'm happy to comply!"

"You are blind to the possibilities Shepard!" The Illusive Man states. "I will make you see just how I intend to control the Reapers!"

The Illusive Man lunges at Shepard with a demonic roar, but Shepard rolls out of the way. He fires a few shots in quick succession and they all hit the Illusive Man square in the back. The Illusive Man shrugs off the shots as if they were nothing, and lunges again.

Shepard slides under the Illusive Man and puts a few more rounds into his chest. The Illusive Man grabs Shepard by the leg and throws him. Shepard smashes into a column with such force that it cracks and he falls to the ground. He gets to his feet and rolls just in time to avoid the Illusive Man's fist.

Shepard tries to fire three shots at the Illusive Man, but only two rounds exit the chamber.

Out of ammo.

Shepard throws the gun at the Illusive Man, and the Illusive Man back hands it away. Shepard activates the Omni-blade and lunges at the Illusive Man. The Illusive Man tries to punch Shepard, but Shepard blocks the blow with the Omni-blade.

The Illusive Man roars and grabs Shepard by the torso and raises him up off the ground. He squeezes and what's left of Shepard's armor starts to crack. "It's inevitable Shepard!" He barks. "The Reapers are the only way that Humanity can evolve!"

"You're so hungry with power…. That you'd risk destroying humanity!" Shepard struggles to speak.

"No! I've saved humanity!" The Illusive Man claims.

"Have you?!" Shepard asks. "Look at what you've done! We are fighting each other… when we should be fighting them!" Shepard feels the Illusive Man's grip tighten. "They even have the Citadel… and it's all because of YOU!"

"I… I have done what is necessary to control the Reapers!" The Illusive Man insists.

"Are you listening to yourself?! You've been indoctrinated!" Shepard shouts, the pressure of the Illusive Man's grip crushing him.

"No, that's not true!" The Illusive Man argues.

"Please… just let me go! I'll do the rest!" Shepard pleads, hoping that the Illusive Man is still in there somewhere. "We can end this! We still have a chance to destroy the Reapers!"

The Illusive Man's grip weakens. "I… no… they're too strong!"

"Fight them! You're stronger!" Shepard barks.

"I can't…. no… I can't…." The Illusive Man roars and his eyes turn red. The Illusive Man is no more, and only the Reapers influence remains. He starts squeezing tighter on Shepard, causing him to grunt in pain.

Suddenly, Shepard hears a weapon fire. A bullet hits the Illusive Man in the side of the head. The Illusive Man roars in pain and weakens his grip on Shepard. Shepard breaks the Illusive Man's grip and falls to the ground, landing on his feet and activating the Omni-blade. He slices across the Illusive Man's chest twice, causing him to stumble backwards.

Shepard quickly searches for who fired the shot, and finds Anderson climbing up the edge of the platform. Satisfied that Anderson is safe, Shepard charges at the Illusive Man and jumps. The Omni-blade activates and Shepard uppercuts the Illusive Man in the chin. The Omni-blade tears through the bottom of the Illusive Man's face and exit's through the top of his head.

Shepard rips the Omni-blade out the front of the Illusive Man's face, and the Illusive Man's lifeless body falls to the ground. Shepard stands up, covered in blood and brain matter. He looks over at Anderson who is still struggling to get up the edge of the platform.

Shepard makes his way over to Anderson. He grabs his hand and starts pulling. "You have got to be the luckiest son of a bitch in space." He jokes.

Shepard pulls Anderson up onto the platform. They both collapse and lay down on their backs. Anderson smirks. "I could say the same thing about you."

Shepard slowly gets to his feet. "No time to rest. We still have some business to take care of." He walks over to the console and presses a few buttons. After a few seconds, the arms of the Citadel slowly start to open.

Meanwhile, out in space, Admiral Hackett watches as the Citadel opens. He flips on his coms. "This is Admiral Hackett. The Citadel is open, prepare the Crucible!"

Back in the Citadel, Shepard walks back over to where Anderson is sitting and sits down next to him. After a few seconds, Shepard finally speaks. "We did it."

"Yes… so we did." Anderson replies. He looks out at Earth. "It's quite a view."

Shepard laughs. "Best seats in the house."

"God." Anderson starts. "It feels like years since I just… sat down."

"I think you've earned a rest." Shepard agrees.

"Damn right I have." Anderson says. He looks over at Shepard. "You did good son. You did good. I'm proud of you."

"Thank you sir." Shepard replies.

"Don't mention it." Anderson says.

They sit there in silence for a few seconds when Shepard gets a hail over his coms.

"Shepard? Commander?" Shepard recognizes the voice as Admiral Hackett's.

"Yes sir?" Shepard responds.

"The Crucible isn't firing. It's got to be something on your end." Hackett explains.

"Alright, standby." Shepard says. He stands up and makes his way over to the console. Anderson follows and watches as Shepard messes with the console. After a few minutes, Shepard slams his hands down on the console in anger. "Damn! I can't find anything!"

Suddenly, the floor beneath Shepard and Anderson shakes and starts to rise up. "What did you do?!" Anderson asks.

"I didn't do this!" Shepard claims. The platform keeps rising up into a shaft. After a few seconds, Shepard and Anderson eventually reach the top. They appear to be out in open space, yet they can still breathe. They both look up and see the massive structure of the Crucible attached to the Citadel.

* * *

(I was too lazy to create the conversation with the starchild here. Will update later, I promise!)

* * *

"Hold on a second." Shepard interrupts. "You're saying that we can destroy the Reapers if we blow up that generator over there?"

"That is correct." The Starchild replies.

"Good to know." Shepard activates his Omni-tool and hails the Normandy. "This is Commander Shepard. Joker, can you hear me?"

Joker's voice comes in over the coms. "I read you Commander."

"I know how to activate the Crucible, but I need you up here to do it!" He explains.

"Roger that Commander! I'll be there in five!" Joker closes the coms.

Anderson walks over to Shepard. "Commander, what are you doing?"

"Your pistol isn't enough to destroy that thing at close range. We would have to get very close to do anything to it, but then we would be killed in the explosion and that isn't very ideal." Shepard explains.

"Then how do you propose we destroy it? The pistol is the only weapon we have." Anderson says.

"No, we have the Normandy." Shepard replies. "We can just blast it once on board."

Suddenly, a red light envelops Shepard and Anderson. They look over at the Starchild, who has changed from a cool blue color to a dark red. "No… this is not how it is supposed to be! You only have three options!"

"Go to hell." Shepard replies.

"If you won't follow the code, then you will die!" The StarChild vanishes, and Husks appear out of nowhere and start attacking. Shepard and Anderson put their backs together and find themselves surrounded.

Shepard activates his Omni-blade. "You take the ones on the left, and I'll take the ones on the right?" Shepard asks jokingly.

The husks lunge at Shepard and Anderson. Shepard starts slashing at Husks, cutting them down one by one. Anderson expertly shoots multiple Husks in the head while occasionally stabbing one with his Omni-Blade.

Without warning, a reaper horn shakes the entire Citadel. Shepard and Anderson look over and see Harbinger rise up and over them. The Husks retreat from their battle with the two soldiers and vanish from sight.

"Harbinger!" Shepard yells. Harbinger's reaper horn roars again.

"You're defeat is inevitable." Harbinger proclaims. "You are facing those who are infinitely your greater." Harbinger extends its arms and starts charging its energy beam. The area around Harbinger starts glowing red as it prepares to fire its laser.

Suddenly, one of Harbinger's arms gets hit by an energy beam. Harbinger roars in rage as the Normandy soars past and lands another direct hit on the arm, causing an explosion that tears the arm apart. "Yeah! Take that you squid looking bastard!" Joker's voice comes on over the coms. "Back up has arrived Commander!" Shepard can't help but smile.

Harbinger fires its beam at the Normandy, but the Normandy gracefully dodges with a barrel roll. Shepard hails Joker over the coms. "Joker, do you think you could distract Harbinger while a shuttle comes and picks us up?"

"With my eyes closed, Commander!" Joker responds. Harbinger misses another shot as the Normandy dips below the massive energy beam. "I'm going to do a fly by and drop off a shuttle."

Ashley's voice comes over the Coms. "I'll do it Joker, I'm the closest to the shuttles! Get us as close as you can!"

Harbinger is smashed by another blast from the Normandy as it does another fly-by. The rear-hatch of the Normandy opens and a shuttle drops out and heads for Anderson and Shepard. A laser from Harbinger just misses the shuttle and slams into the Crucible.

Shepard looks at the Crucible with intensity. "We can't let the Crucible get hit like that again! It's our only hope of stopping the Reapers!"

Anderson hails Tali on the coms. "Tali, do you think you could re-direct some of your forces to distract Harbinger?"

Tali's voice comes onto the coms. "No good Admiral. We're too busy fighting other Reapers!"

The shuttle lands right next to Shepard and Anderson. The hatches swing open and Ashley's voice echoes on the outer speakers. "Get in!"

Shepard and Anderson dash on board as the hatch swings shut behind them. They walk into the cockpit and Anderson looks at Ashley. "Let me drive, Williams. Joker and I have a maneuver we've worked on for just such an occasion."

"Yes sir!" Ashley jumps out of the pilot's seat and into Shepard's arms. Shepard returns her affection with a kiss. "I thought I would never see you again."

Anderson rolls his eyes, smirks, and gets into the pilot's seat. The shuttle rises up and rockets away from the Crucible. Anderson hails Joker over the coms. "Joker, remember the Meteor Twist?" He asks.

"I sure do Admiral! I'm getting in possession now!" Joker assures.

The Normandy rockets towards the shuttle. Shepard and Ashley look on in quite concern. "Um… Anderson? What are you doing?" Shepard asks. Anderson ignores Shepard and keeps the shuttle on a collision course with the Normandy.

At the last second, the Normandy does a 180 and opens its rear hatch. The shuttle also does a 180 and Anderson pushes the throttle to full power. The shuttle slams into the cargo bay at full speed, knocking over a MAKO tank and damaging other shuttles. Shepard and Ashley fall over as the Shuttle grinds to a halt in the cargo bay. "Joker, we're on board! Blast Harbinger with everything we've-"

"Wait!" Shepard interrupts. "Ignore Harbinger! He's not our primary target!"

Joker's voice sounds confused over the coms. "Wait… you don't want me to shoot at the giant Reaper that's shooting at us?"

"Hold on, I'm giving you a firing solution." Shepard activates his Omni-tool and gives Joker the coordinates for the generator.

"Umm… Commander, this says that I'm shooting the Crucible?" Joker asks, slightly concerned.

"I need you to trust me Joker." Shepard insists.

There is a short pause before Joker speaks over the coms. "Yes sir Commander. Firing on the target for effect."

The Normandy dodges another laser from Harbinger and heads straight for the Crucible. Joker prepares a single missile for the red generator.

When they get to the bridge, Shepard, Ashley, and Anderson dash through the door and over to Joker. EDI looks over and smiles. "It is good to see you again Shepard."

Shepard looks at EDI. "Nice to see you too. I actually have to ask you to do something."

"Oh? What is that, Commander?" EDI asks, curious to what the human could want at a time like this.

"Is there a way for you to break yourself into pieces of code that can be put back together later with a simple command?" Shepard asks.

"Theoretically, yes. Why?" EDI replies.

"When Joker destroys that generator, the Crucible is going to activate and destroy any synthetic life in the galaxy-" Shepard starts to explain.

"But being in small pieces of code will keep me intact for later activation." EDI finishes for him. "I will send the word out to the fleet before I begin the process."

The Normandy gets a direct hit on the top of the ship from Harbinger's laser. The shields take most of the blast, but the outer hull is badly damaged.

The Normandy shakes violently, nearly knocking everyone off their feet. "Commander, there was a hull breach in your quarters!" Joker tells him.

"Everything that's lost can be replaced! Just focus on the Crucible!" Shepard says. Although he doesn't admit it, there were things in that cabin that were very precious to him.

EDI sends the message to all ships in the system before looking at Joker. "I hope this works so that I may see you again." Joker nods, and EDI deactivates, causing her body to slump in the seat.

Joker looks forwards with fire in his eyes. "Alright you Reaper bastards, take this!"

The Normandy fires the missile at the Crucible before doing a barrel roll and flying away from it. The missile impacts with incredible force, and the generator detonates. Red energy surges from the Crucible and into the Citadel.

"Joker, get us out of here!" Shepard orders.

Admiral Hackett's voice comes on over the coms. "All fleets, the Crucible is armed! Disengage and head for the rendezvous point!"

The Normandy makes a sharp turn and jumps out from view with thousands of other ships. Meanwhile, the Crucible's energy field grows and consumes Earth with its red embrace. Harbinger is the first to be destroyed by the blast; its horn roars one last time. One by one, the rest of the Reapers on Earth follow and ground forces cheer at their demise.

The energy from the Citadel condenses in a single point before launching the energy out to the edge of the Sol system. In a matter of seconds, it reaches the Mass Relay and fires out into the blackness of space. This causes a domino effect as the energy from the Crucible scatters across the galaxy, using the Mass Relays as conduits.

Back on the Normandy, Joker struggles to keep the Normandy ahead of the energy field. He pushes the Normandy's mass effect core to its very limit, but it still isn't enough. Joker overrides the security protocols in the mass effect core and pushes the Normandy even harder.

"Come on, baby, don't give up on me now!" He pleads. Equipment on the Normandy sparks from the pressure of the mass effect core, but Joker keeps the Normandy going. The energy from the Crucible eventually catches up with them and engulfs the entire ship. The mass effect core fails and systems go offline as the Normandy rockets uncontrollably towards an unidentified planet.

"Attention all hands, brace for impact!" Joker speaks over the ship's coms system.

Shepard grabs Ashley and buckles her into a nearby navigation chair before buckling himself in right next to her. Anderson buckles himself in on the opposite side of Joker. "Damn! I can't get the systems back online!" Joker yells. He buries his face in his hands. "The Normandy won't be able to handle a crash like this!"

Suddenly, power is restored to the Normandy and the navigation systems are back online. Joker feels a hand on his shoulder and looks over to see EDI smiling. "EDI! You're alive!" Joker says excitedly.

"You might want to stop the Normandy from crashing into the planet." EDI says with a surprisingly human tone.

"Oh, right." Joker says. He activates the navigation system and once again takes control of the Normandy.

The Normandy enters the planet's atmosphere upside down and friction starts to heat up the outer hull. Before too much damage is sustained, the Normandy flips over right-side-up. Joker turns the bottom thrusters to maximum burn and the Normandy starts to slow down.

The Normandy smashes into the ground and slides for over five hundred yards, destroying anything in its path. The Normandy finally comes to a stop near the edge of a cliff, causing some boulders and trees to fall.

Shepard slowly opens his eyes, dazed from the trauma of planet entry. He looks over at Ashley and sees that she has a gash on her head; blood flowing down her face. She has her eyes closed, which isn't good. Shepard gently shakes her for a few seconds and is relived when she starts opening her eyes.

Satisfied that Ashley is safe, Shepard looks to Anderson. The only injury Shepard can make out on Anderson is a busted lip, but other than that he appears to be fine. Anderson looks at Shepard and laughs weakly. Shepard smirks before looking over to the cockpit.

Joker is looking around, dazed. EDI is looking over the ship's systems. "EDI, what's our status?" Shepard asks.

"The Normandy's outer hull integrity is at 43%, and the Mass Effect core has sustained minor damage. Thrusters two and three have sustained heavy damage, but they are repairable." EDI reports.

"What about crew?" Shepard requests, concerned.

EDI is silent for a moment, no doubt scanning the ship. "There are minor injuries, but no casualties." EDI replies. Shepard breathes a sigh of relief. He unhooks himself from the chair and walks over to the cockpit. He puts his hand on Joker's shoulder.

"Did I ever tell you how much you suck at piloting? " Shepard jokes.

"I'm a handicap, what do you want from me?" They both smirk.

Shepard looks over at EDI. "EDI, is the air out there breathable?"

"Scanning…" EDI uses the ships outer sensors to find out what is in the air. "The air is almost identical to Earth's atmosphere, consisting of 78% nitrogen, 21% oxygen, and 0.3% carbon dioxide."

"Good." Shepard replies. "Open a channel to the entire ship."

Joker presses a few buttons before nodding at Shepard.

"This is Commander Shepard to all hands. I think you've all deserved a break, so before we begin repairs on the Normandy, I'm giving you an hour to rest. Good work people." Shepard nods and Joker turns off the channel.

EDI helps Joker out of the chair and over to the Normandy's hatch. Joker punches in the secure key and the hatch glides open. The sunlight blinds Joker for a split second as he steps out of the Normandy and onto the soft dirt.

EDI pokes her head out of the hatch and looks around at the unexplored planet's foliage. Joker holds out his hand and EDI takes it to let him help her down.

Shepard unhooks Ashley from her chair and helps her up. "Are you alright Ash?" He asks.

"Yeah… my head just hurts a little." She says weakly. She attempts to walk on her own, but the pain in her head is too much and she stumbles. Luckily, Shepard catches her just in time.

"I've got you." Shepard picks up Ashley princess style and makes his way over to the elevator.

"Wait." Ashley starts. "I want to go outside first."

"Ash, you need medical attention and-"

"So do you." Ashley interrupts with a smile. Shepard sighs and carries Ashley outside. They are both blinded by the light for a moment before seeing the breathtaking view of the new planet.

"It's beautiful." Ashley comments.

"Yeah." Shepard agrees.

Liara comes out of the ship with haste. "Shepard?" Shepard and Ashley pull apart and smirk for a second. "Admiral Hackett is on the line. He wants to know if the Normandy would be able to meet back up with the fleet?"

"Tell him the ship just needs some minor repairs and we'll be on our way." Shepard says.

"Of course." Liara replies before going back into the ship.

Shepard looks at Ashley, who is still in his arms. "Could be a great place to set up a home, huh?"

Ashley looks at Shepard in surprise. "What are you… wait… you mean?"

Shepard leans in and kisses Ashley. Ashley returns the kiss passionately. For the first time in months, they can enjoy each other's company without the threat of the Reapers looming over their heads.

* * *

**WAHBAM! What do you think about that? Don't get me wrong, I love the Mass Effect Trilogy, but I always thought that the ending needed something. I've written it in such a way that you could almost imagine yourself playing it. Starting with the Illusive Man boss fight, then having the fight on top of the Citadel with all of the husks.**

**And before you ask, yes I romance Ashley. I've just always thought that Shepard and Ashley go together perfectly.**

**And don't worry children; I'll update the conversation between the Starchild and Shepard later. I just need to finish Leviathen first, just in case there's something I could use. =D**

**I might actually make a storyline after this just for fun, depending on the reviews.**

**I hope you enjoyed my interpretation of Mass Effect 3's ending, and I hope that you're looking forward to my other chapters of "Halo 4: A Rip in Time". GOOD NIGHT CHILDREN!**


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